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Detailed information for vg0208784668:

Variant ID: vg0208784668 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8784668
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTTTCAACTTTCAGTTCAGAAAGGGCTTTGTGTTCAACATGCGCGGTCGCCCACTCCCACGGTCATCTACATCTAAGCATGTGGATCTCCCTCCACTC[G/A]
TTTTCTGCGTGCATAATTCCCAAACTGCCGATGTGTTCTTTAAAAAAAGTTTCTATACGAAAGTTACTTAAAAAAATCATATTGTTCTATTTTTTTAAAA

Reverse complement sequence

TTTTAAAAAAATAGAACAATATGATTTTTTTAAGTAACTTTCGTATAGAAACTTTTTTTAAAGAACACATCGGCAGTTTGGGAATTATGCACGCAGAAAA[C/T]
GAGTGGAGGGAGATCCACATGCTTAGATGTAGATGACCGTGGGAGTGGGCGACCGCGCATGTTGAACACAAAGCCCTTTCTGAACTGAAAGTTGAAACTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.50%	15.50%	0.02%	0.00%	NA
All Indica	2759	82.00%	18.00%	0.00%	0.00%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	25.30%	74.30%	0.37%	0.00%	NA
Indica I	595	71.80%	28.20%	0.00%	0.00%	NA
Indica II	465	66.70%	33.30%	0.00%	0.00%	NA
Indica III	913	94.10%	5.90%	0.00%	0.00%	NA
Indica Intermediate	786	84.70%	15.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208784668	G -> A	LOC_Os02g15620.1	downstream_gene_variant ; 3045.0bp to feature; MODIFIER	silent_mutation	Average:89.083; most accessible tissue: Minghui63 root, score: 97.42	N	N	N	N
vg0208784668	G -> A	LOC_Os02g15630.1	intron_variant ; MODIFIER	silent_mutation	Average:89.083; most accessible tissue: Minghui63 root, score: 97.42	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0208784668	G	A	-0.04	-0.02	-0.01	0.01	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208784668	NA	4.20E-06	mr1185	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0208784668	NA	7.71E-08	mr1392	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0208784668	NA	2.08E-07	mr1420	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0208784668	NA	5.08E-07	mr1507	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0208784668	NA	6.82E-07	mr1556	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0208784668	NA	2.21E-07	mr1764	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0208784668	NA	1.93E-08	mr1884	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0208784668	NA	6.46E-06	mr1952	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251